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Calcium in PDB 3s9w: Crystal Structure of Staphylococcal Nuclease Variant Delta+Phs M98G Bound to CA2+ and Thymidine-5',3'-Diphosphate at Cryogenic Temperature

Enzymatic activity of Crystal Structure of Staphylococcal Nuclease Variant Delta+Phs M98G Bound to CA2+ and Thymidine-5',3'-Diphosphate at Cryogenic Temperature

All present enzymatic activity of Crystal Structure of Staphylococcal Nuclease Variant Delta+Phs M98G Bound to CA2+ and Thymidine-5',3'-Diphosphate at Cryogenic Temperature:
3.1.31.1;

Protein crystallography data

The structure of Crystal Structure of Staphylococcal Nuclease Variant Delta+Phs M98G Bound to CA2+ and Thymidine-5',3'-Diphosphate at Cryogenic Temperature, PDB code: 3s9w was solved by B.M.Doctrow, J.L.Schlessman, B.Garcia-Moreno E., A.Heroux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.30 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 31.207, 60.531, 38.354, 90.00, 93.13, 90.00
R / Rfree (%) 17.1 / 21.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Staphylococcal Nuclease Variant Delta+Phs M98G Bound to CA2+ and Thymidine-5',3'-Diphosphate at Cryogenic Temperature (pdb code 3s9w). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of Staphylococcal Nuclease Variant Delta+Phs M98G Bound to CA2+ and Thymidine-5',3'-Diphosphate at Cryogenic Temperature, PDB code: 3s9w:

Calcium binding site 1 out of 1 in 3s9w

Go back to Calcium Binding Sites List in 3s9w
Calcium binding site 1 out of 1 in the Crystal Structure of Staphylococcal Nuclease Variant Delta+Phs M98G Bound to CA2+ and Thymidine-5',3'-Diphosphate at Cryogenic Temperature


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Staphylococcal Nuclease Variant Delta+Phs M98G Bound to CA2+ and Thymidine-5',3'-Diphosphate at Cryogenic Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca150

b:22.6
occ:1.00
 OD1 A:ASP40 2.8 19.5 1.0
O A:THR41 2.8 20.1 1.0
OD2 A:ASP21 2.9 20.9 1.0
O A:HOH186 2.9 14.2 1.0
O A:HOH174 3.0 15.4 1.0
OE2 A:GLU43 3.1 33.6 1.0
O4P A:THP151 3.2 23.0 1.0
O A:HOH216 3.6 21.7 1.0
CG A:ASP21 3.7 19.7 1.0
OD1 A:ASP21 3.8 17.7 1.0
CG A:ASP40 3.9 20.9 1.0
C A:THR41 3.9 19.9 1.0
CD A:GLU43 4.0 32.6 1.0
O A:HOH210 4.0 22.2 1.0
N A:THR41 4.0 14.8 1.0
OG1 A:THR41 4.1 17.3 1.0
NH2 A:ARG35 4.1 17.9 1.0
O A:HOH211 4.1 12.8 1.0
O5P A:THP151 4.2 19.0 1.0
P2 A:THP151 4.2 19.7 1.0
CA A:THR41 4.5 18.4 1.0
OD2 A:ASP40 4.6 25.1 1.0
CA A:ASP40 4.6 15.6 1.0
C A:ASP40 4.6 15.9 1.0
O6P A:THP151 4.6 20.9 1.0
OE1 A:GLU43 4.7 31.6 1.0
O A:HOH173 4.7 18.1 1.0
O A:HOH196 4.7 18.3 1.0
CZ A:ARG35 4.7 19.1 1.0
C A:PRO42 4.8 24.7 1.0
CG A:GLU43 4.8 30.5 1.0
NE A:ARG35 4.8 16.1 1.0
O A:PRO42 4.8 25.4 1.0
N A:GLU43 4.9 25.1 1.0
CB A:ASP40 4.9 15.6 1.0
CB A:THR41 4.9 19.1 1.0

Reference:

B.M.Doctrow, J.L.Schlessman, B.Garcia-Moreno E.. Crystal Structure of Staphylococcal Nuclease Variant Delta+Phs M98G Bound to CA2+ and Thymidine-5',3'-Diphosphate at Cryogenic Temperature To Be Published.
Page generated: Tue Jul 8 16:34:07 2025

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